moving log file output to before the assert statement, so we can more easily see which file is missing [if a file is missing]

moving the check for the "live" flag into the runProcess function, so will be picked up when not running directly from the command line

Optional config argument to delete mid-process files at the end of a
successful job. There is an associated command-line flag '--clearup'.

The reason for this feature is to provide a way to slim down data
volumes of production runs. A lot of processing files are generated
and production runs may only need to retain configuration, logs and
outputs. Also, the inputs might be archived separately, so they
wouldn't need to be retained in prod runs.

Currently, files are moved to a hard-coded 'recycling bin' directory,
and there is a minimal set of files set for clearup: only the deposition
and environment tar files.

This change requires some standard structure to outputs of
processor_in_job functions, which would be more robust if
a class structure is implemented.

TODO: Implement a test for file clearup.

chore: Tidy imports

This is necessary for Win to be able to rename the file afterward.

1) There is now a python alternative to the R-based wheat-source-
generation, called source_gen. The functionality to call source_gen
has been added (see ProcessorSurveys.pyL939 and L1032-1040), but not
yet switched on while we await testing of
output at the Met Office.

2) ProcessorComponents was huge (2100 lines!) and the structure was
not apparent. Each component's supporting functions are now in a
separate directory. There is also a ProcessorServer.py relating to
file down/up-loads. ProcessorComponents is now essentially a directory
 to import all the functions. This might inspire a more systematic
 (object-oriented?) structure for each component within coordinator
 in the future.

reading NAME.nc files rather than NAME.txt files (#19)

And some logging messages have had their level changed.

The email config is required to set up the logging before any other
tasks are done in order to maximise coverage. It is expected that the
location of the required config file is defined in run_Processor.sh,
or exported to local environment before calling Processor.py.

The ssh commands now do not check new server identities. This prevents a
user prompt on first-time use, which otherwise inhibits Amazon Web
Server instances.

10-buffer-logging-emails-and-send-at-end-of-script-or-hit-an-uncaught-exception-2

The newly imported AdvisoryBuilder can be run separately, see
that project for more details.
Updated conda environment accordingly.

This configuration works with EWS-EpiModel git commit 631e3520. This can handle multiple diseases but only one region. Output directories are <job-directory>/<region>/<disease>/<output>

Back run handling. If env.suit. results are available in a _bak folder, copy results from the _bak folder and skip env.suit. calc.

This should only apply to the operational copy of the EWS-Coordinator. If you want to run a separate copy for any reason, make these changes to point to your separate workspace. The git ignored files still need pointing to, but they don't need to be duplicated. Your local version of these changes can be stashed while pushing and pulling to/from the master branch.

In operational version, this is needed for survey results. The way this is implemented, it can be configured for any other component too.